I recently purchased a cooler master 690 ii advanced (in spite of some warnings on these forums) and I have to agree its not a quiet case. For now I'm just focusing on getting the system up and running without putting too much effort into silencing it so there's no doubt room for improvement but it will be a while before I get around to it all (though I hope to report back).
Right now its running the three stock fans that come with the case (2x140 and 1x120) and the stock fan of my Scythe Mugen 2 cooler. I haven't put a lot of effort into controlling the fan speeds yet but I'm wondering what some reasonable numbers would be. The case fans are running at around 450, 750, and 800 rpms (not sure which is which) while the cpu fan is around 1100 rpm I guess (though these numbers might be mixed up). My core temps are around 30-40 C and my gpu temp is around 30 C so I guess I'm over-cooling this system. For my specs check this thread:viewtopic.php?f=15&t=62152
The system as it is is noisy. The fans generate a noticeable background whir and the HD is quite noisy when active (unfortunately I could only get hold of the WD black edition though I was planning to get a blue one). I can live with the HD noise but would like to maybe slow down the fans a bit and even disable one. The CM 690 has a front fan, a back fan and a fan on top. Along with the scythe mugen fan that's probably too many. Would it make sense to disable to the fan on the top of the case and slow the others down? What would be reasonable fan speeds (assuming the bios gives me enough control)? What temperatures should I aim for before I worry?